1. Benchmark of electronic structure methods for protein–ligand interactions based on high-level reference data
- Author
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Tobias Schwabe, Pascal Heitel, Martin Korth, and Nusret Duygu Yilmazer
- Subjects
Chemistry ,Reference data (financial markets) ,Ab initio ,Context (language use) ,Electronic structure ,Computer Science Applications ,Test case ,Computational Theory and Mathematics ,Computational chemistry ,Benchmark (computing) ,Density functional theory ,Physical and Theoretical Chemistry ,Algorithm ,Protein ligand - Abstract
The accurate prediction of the strength of protein–ligand interactions is a very difficult problem despite impressive advances in the field of biomolecular modeling. There are good reasons to believe that quantum mechanical methods can help with this task, but the application of such methods in the context of scoring is still in its infancy. Here we benchmark several wave function theory (WFT), density functional theory (DFT) and semiempirical quantum mechanical (SQM) approaches against high-level theoretical references for realistic test cases. Based on our findings for systematically generated model systems of real protein/ligand complexes from the PDB-bind database, we can recommend SCS-MP2 and B2-PLYP-D3 as reference methods, TPSS-D3+Dabc/def-TZVPP as the best DFT approach and PM6-DH+ as a fast and accurate alternative to full ab initio treatments.
- Published
- 2015
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